Method for treating cancer

ABSTRACT

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.13/164,499, filed Jun. 20, 2011, which claims priority to U.S.Provisional Application Ser. No. 61/356,501 filed Jun. 18, 2010, theentire contents of each of which are hereby incorporated by reference.

BACKGROUND 1. Technical Field

This document relates to methods and materials involved in assessingsamples (e.g., cancer cells) for the presence of a loss ofheterozygosity (LOH) signature. For example, this document providesmethods and materials for determining whether or not a cell (e.g., acancer cell) contains an LOH signature. This document also providesmaterials and methods for identifying cells (e.g., cancer cells) havinga deficiency in homology directed repair (HDR) as well as materials andmethods for identifying cancer patients likely to respond to aparticular cancer treatment regimen.

2. Background Information

Cancer is a serious public health problem, with 562,340 people in theUnited States of America dying of cancer in 2009 alone. American CancerSociety, Cancer Facts & Figures 2009 (available at American CancerSociety website). One of the primary challenges in cancer treatment isdiscovering relevant, clinically useful characteristics of a patient'sown cancer and then, based on these characteristics, administering atreatment plan best suited to the patient's cancer. While strides havebeen made in this field of personalized medicine, there is still asignificant need for better molecular diagnostic tools to characterizepatients' cancers.

SUMMARY

This document provides methods and materials involved in assessingsamples (e.g. cancer cells) for the presence of a loss of heterozygosity(LOH) signature. For example, this document provides methods andmaterials for determining whether or not a cell (e.g., cancer cell)contains an LOH signature. An LOH signature as used herein refers to thepresence of five or more (e.g., six or more, seven or more, eight ormore, nine or more, ten or more, eleven or more, 12 or more, 13 or more,14 or more, 15 or more, 16 or more, 17 or more, 18 or more, 19 or more,or 20 or more) LOH regions that are longer than about 1.5 megabases(e.g., longer than about 2, 2.5, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13,14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50, 75, or 100 megabases(Mb)) and are less than the length of the entire chromosome thatcontains that LOH region. In general, all the chromosomes of a genomefor a sample (e.g., tumor biopsy) can be assessed for the presence of anLOH signature. In some cases, all the chromosomes of a genome for asample with the exception of chromosome 17 can be assessed for thepresence of an LOH signature. For males only autosomal chromosomes canbe assessed for the presence of an LOH signature.

As described herein, cancer cells having a genome containing an LOHsignature can be identified as being likely to have a deficiency inhomology directed repair (HDR). In some cases, cancer cells having agenome containing an LOH signature can be identified as being likely tohave a deficient status in one or more genes involved in HDR. Forexample, cancer cells having a genome containing an LOH signature can beidentified as being likely to have a deficient BRCA1 or BRCA2 status,and cells having a genome lacking an LOH signature can be identified asbeing likely to have an intact BRCA1 or BRCA2 status.

Determining whether a cell (e.g., a cancer cell) is likely to have adeficiency in HDR or is likely to have a deficient status in one or moregenes involved in HDR can indicate that the mammal (e.g., human) withthat cell is likely to have one or more genetic defects within themammal's germline. Identifying humans with an increased likelihood ofhaving such a germline defect can allow the human or clinicians toinform offspring of the possible inheritance of such a germline defect.Such offspring can elect, based at least in part on such information, toundergo genetic testing and possible monitoring (e.g., early detectionmonitoring) for the development of cancer.

As also described herein, cancer cells having a genome containing an LOHsignature can be identified as being likely to respond to a particularcancer treatment regimen. For example, patients having cancer cells witha genome containing an LOH signature can be identified as being likelyto respond to a cancer treatment regimen that includes the use of a DNAdamaging agent, a PARP inhibitor, radiation, or a combination thereof.In some cases, patients having cancer cells with a genome lacking an LOHsignature can be identified as being unlikely to respond to a cancertreatment regimen designed to administer a single agent such as a singleDNA damaging agent, a single PARP inhibitor, or radiation alone. In somecases, patients having cancer cells with a genome lacking an LOHsignature can be identified as being likely to respond to a cancertreatment regimen that includes the use of a standard cancer treatmentagent not associated with HDR (e.g., a taxol compound such aspaclitaxel).

Determining whether or not cancer patients are likely to respond to aparticular cancer treatment regimen as described herein can allowpatients and clinicians to proceed with a treatment regimen having anincreased likelihood of treating cancer (e.g., reducing the number ofcancer cells within a patient). In some cases, determining whether ornot cancer patients are likely to respond to a particular cancertreatment regimen as described herein can allow patients and cliniciansto select the most effective initial cancer treatment regimen for thatpatient.

In general, one aspect of this document features a method for assessingLOH in a cancer cell or genomic DNA thereof. The method comprises, orconsists essentially of, (a) detecting, in a cancer cell or genomic DNAderived therefrom, LOH regions in at least one pair of human chromosomesof the cancer cell, wherein the at least one pair of human chromosomesis not a human X/Y sex chromosome pair; and (b) determining the totalnumber of LOH regions, in the at least one pair of human chromosomes,that are longer than a first length but shorter than the length of thewhole chromosome containing the LOH region, wherein the first length isabout 1.5 or more megabases.

In another aspect, this document features a method of predicting thestatus of BRCA1 and BRCA2 genes in a cancer cell. The method comprises,or consists essentially of, determining, in the cancer cell, the totalnumber of LOH regions in at least one pair of human chromosomes of thecancer cell that are longer than a first length but shorter than thelength of the whole chromosome containing the LOH region, wherein the atleast one pair of human chromosomes is not a human X/Y sex chromosomepair, wherein the first length is about 1.5 or more megabases; andcorrelating the total number that is greater than a reference numberwith an increased likelihood of a deficiency in the BRCA1 or BRCA2 gene.

In another aspect, this document features a method of predicting thestatus of HDR in a cancer cell. The method comprises, or consistsessentially of, determining, in the cancer cell, the total number of LOHregions in at least one pair of human chromosomes of the cancer cellthat are longer than a first length but shorter than the length of thewhole chromosome containing the LOH region, wherein the at least onepair of human chromosomes is not a human X/Y sex chromosome pair,wherein the first length is about 1.5 or more megabases; and correlatingthe total number that is greater than a reference number with anincreased likelihood of a deficiency in HDR.

In another aspect, this document features a method of predicting acancer patient's response to a cancer treatment regimen comprising a DNAdamaging agent, an anthracycline, a topoisomerase I inhibitor,radiation, and/or a PARP inhibitor. The method comprises, or consistsessentially of, determining, in a cancer cell from the cancer patient,the number of LOH regions in at least one pair of human chromosomes of acancer cell of the cancer patient that are longer than a first lengthbut shorter than the length of the whole chromosome containing the LOHregion, wherein the at least one pair of human chromosomes is not ahuman X/Y sex chromosome pair, wherein the first length is about 1.5 ormore megabases; and correlating the total number that is greater than areference number with an increased likelihood that the cancer patientwill respond to the cancer treatment regimen.

In another aspect, this document features a method of predicting acancer patient's response to a treatment regimen. The method comprises,or consists essentially of, determining, in a cancer cell from thecancer patient, the total number of LOH regions in at least one pair ofhuman chromosomes of a cancer cell of the cancer patient that are longerthan a first length but shorter than the length of the whole chromosomecontaining the LOH region, wherein the at least one pair of humanchromosomes is not a human X/Y sex chromosome pair, wherein the firstlength is about 1.5 or more megabases; and correlating the total numberthat is greater than a reference number with an increased likelihoodthat the cancer patient will not respond to a treatment regimenincluding paclitaxel or docetaxel.

In another aspect, this document features a method of treating cancer.The method comprises, or consists essentially of, (a) determining, in acancer cell from a cancer patient or genomic DNA obtained therefrom, thetotal number of LOH regions in at least one pair of human chromosomes ofthe cancer cell that are longer than a first length but shorter than thelength of the whole chromosome containing the LOH region, wherein the atleast one pair of human chromosomes is not a human X/Y sex chromosomepair, wherein the first length is about 1.5 or more megabases; and (b)administering to the cancer patient a cancer treatment regimencomprising one or more drugs chosen from the group consisting of DNAdamaging agents, anthracyclines, topoisomerase I inhibitors, and PARPinhibitors, if the total number of LOH regions is greater than areference number.

For any one or more of the methods described in the preceding sixparagraphs, any one or more of the following can be applied asappropriate. The LOH regions can be determined in at least two, five,ten, or 21 pairs of human chromosomes. The cancer cell can be anovarian, breast, or esophageal cancer cell. The total number of LOHregions can be 9, 15, 20 or more. The first length can be about 6, 12,or 15 or more megabases. The reference number can be 6, 7, 8, 9, 10, 11,12, 13, or greater. The at least one pair of human chromosomes canexclude human chromosome 17. The DNA damaging agent can be cisplatin,carboplatin, oxalaplatin, or picoplatin, the anthracycline can beepirubincin or doxorubicin, the topoisomerase I inhibitor can becampothecin, topotecan, or irinotecan, or the PARP inhibitor can beiniparib, olaparib or velapirib.

In another aspect, this document features the use of one or more drugsselected from the group consisting of DNA damaging agents,anthracyclines, topoisomerase I inhibitors, and PARP inhibitors, in themanufacture of a medicament useful for treating a cancer in a patientidentified as having a cancer cell determined to have a total of 5 ormore Indicator LOH Regions. The Indicator LOH Regions can be determinedin at least two, five, ten, or 21 pairs of human chromosomes. The cancercell can be an ovarian, breast, or esophageal cancer cell. The totalnumber of Indicator LOH Regions can be 9, 15, 20 or more. The IndicatorLOH Regions can have a length of about 6, 12, or 15 or more megabases.The Indicator LOH Regions can be present on a chromosome other thanhuman chromosome 17. The DNA damaging agent can be a platinum-basedchemotherapy drug, the anthracycline can be epirubincin or doxorubicin,the topoisomerase I inhibitor can be campothecin, topotecan, oririnotecan, or the PARP inhibitor can be iniparib, olaparib orvelapirib.

In another aspect, this document features the use of a plurality ofoligonucleotides capable of hybridizing to a plurality of polymorphicregions of human genomic DNA, in the manufacture of a diagnostic kituseful for determining the total number of Indicator LOH Regions in atleast a chromosome pair of a human cancer cell obtained from a cancerpatient, and for detecting (a) an increased likelihood of a deficiencyin the BRCA1 or BRCA2 gene in the cancer cell, (b) an increasedlikelihood of a deficiency in HDR in the cancer cell, or (c) anincreased likelihood that the cancer patient will respond to cancertreatment regimen comprising a DNA damaging agent, an anthracycline, atopoisomerase I inhibitor, radiation, or a PARP inhibitor. The IndicatorLOH Regions can be determined in at least two, five, ten, or 21 pairs ofhuman chromosomes. The cancer cell can be an ovarian, breast, oresophageal cancer cell. The total number of Indicator LOH Regions can be9, 15, 20 or more. The Indicator LOH Regions can have a length of about6, 12, or 15 or more megabases. The Indicator LOH Regions can be presenton a chromosome other than human chromosome 17.

In another aspect, this document features a system for determining LOHstatus of a cancer cell of a cancer patient. The system comprises, orconsists essentially of, (a) a sample analyzer configured to produce aplurality of signals about genomic DNA of at least one pair of humanchromosomes of the cancer cell, and (b) a computer sub-system programmedto calculate, based on the plurality of signals, the number of IndicatorLOH Regions in the at least one pair of human chromosomes. The computersub-system can be programmed to compare the number of Indicator LOHRegions to a reference number to determine (a) a likelihood of adeficiency in BRCA1 and/or BRCA2 genes in the cancer cell, (b) alikelihood of a deficiency in HDR in the cancer cell, or (c) alikelihood that the cancer patient will respond to cancer treatmentregimen comprising a DNA damaging agent, an anthracycline, atopoisomerase I inhibitor, radiation, or a PARP inhibitor. The systemcan comprise an output module configured to display the likelihood of(a), (b), or (c). The system can comprise an output module configured todisplay a recommendation for the use of the cancer treatment regimen.The Indicator LOH Regions can be determined in at least two, five, ten,or 21 pairs of human chromosomes. The cancer cell can be an ovarian,breast, or esophageal cancer cell. The total number of Indicator LOHRegions can be 9, 15, 20, or more. The Indicator LOH Regions can have alength of about 6, 12, or 15 or more megabases. The Indicator LOHRegions can be present on chromosomes other than a human chromosome 17.The DNA damaging agent can be a platinum-based chemotherapy drug, theanthracycline can be epirubincin or doxorubicin, the topoisomerase Iinhibitor can be campothecin, topotecan, or irinotecan, or the PARPinhibitor can be iniparib, olaparib or velapirib.

In another aspect, this document features a computer program productembodied in a computer readable medium that, when executing on acomputer, provides instructions for detecting the presence or absence ofany LOH region along one or more of human chromosomes other than thehuman X and Y sex chromosomes, and the LOH region having a length ofabout 1.5 or more megabases but shorter than the length of the wholechromosome containing the LOH region; and determining the total numberof the LOH region in the one or more chromosome pairs. The computerprogram product can include other instructions. The Indicator LOHRegions can be determined in at least two, five, ten or 21 pairs ofhuman chromosomes. The cancer cell can be an ovarian, breast, oresophageal cancer cell. The total number of Indicator LOH Regions can be9, 15, 20, or more. The Indicator LOH Regions can have a length of about6, 12, or 15 or more megabases. The Indicator LOH Regions can be presenton chromosomes other than a human chromosome 17. The DNA damaging agentcan be a platinum-based chemotherapy drug, the anthracycline can beepirubincin or doxorubicin, the topoisomerase I inhibitor can becampothecin, topotecan, or irinotecan, or the PARP inhibitor can beiniparib, olaparib or velapirib.

In another aspect, this document features a diagnostic kit. The kitcomprises, or consists essentially of, at least 500 oligonucleotidescapable of hybridizing to a plurality of polymorphic regions of humangenomic DNA; and a computer program product provided herein. Thecomputer program product can be embodied in a computer readable mediumthat, when executing on a computer, provides instructions for detectingthe presence or absence of any LOH region along one or more of humanchromosomes other than the human X and Y sex chromosomes, and the LOHregion having a length of about 1.5 or more megabases but shorter thanthe length of the whole chromosome containing the LOH region; anddetermining the total number of the LOH region in the one or morechromosome pairs. The computer program product can include otherinstructions. In another aspect, this document features a method forassessing cancer cells of a patient for the presence of an LOHsignature. The method comprises, or consists essentially of, (a)detecting the presence of more than a reference number of LOH regions inat least one pair of human chromosomes of a cancer cell of the cancerpatient that are longer than a first length but shorter than the lengthof the whole chromosome containing the LOH region, wherein the at leastone pair of human chromosomes is not a human X/Y sex chromosome pair,wherein the first length is about 1.5 or more megabases, and (b)identifying the patient as having cancer cells with the LOH signature.

In another aspect, this document features a method for assessing cancercells of a patient for the presence of an HDR deficient status. Themethod comprises, or consists essentially of, (a) detecting the presenceof more than a reference number of LOH regions in at least one pair ofhuman chromosomes of a cancer cell of the cancer patient that are longerthan a first length but shorter than the length of the whole chromosomecontaining the LOH region, wherein the at least one pair of humanchromosomes is not a human X/Y sex chromosome pair, wherein the firstlength is about 1.5 or more megabases, and (b) identifying the patientas having cancer cells with the HDR deficient status.

In another aspect, this document features a method for assessing cancercells of a patient for the presence of a genetic mutation within a genefrom an HDR pathway. The method comprises, or consists essentially of,(a) detecting the presence of more than a reference number of LOHregions in at least one pair of human chromosomes of a cancer cell ofthe cancer patient that are longer than a first length but shorter thanthe length of the whole chromosome containing the LOH region, whereinthe at least one pair of human chromosomes is not a human X/Y sexchromosome pair, wherein the first length is about 1.5 or moremegabases, and (b) identifying the patient as having cancer cells withthe genetic mutation.

In another aspect, this document features a method for determining if apatient is likely to respond to a cancer treatment regimen comprisingadministering radiation or a drug selected from the group consisting ofDNA damaging agents, anthracyclines, topoisomerase I inhibitors, andPARP inhibitors. The method comprises, or consists essentially of, (a)detecting the presence of more than a reference number of LOH regions inat least one pair of human chromosomes of a cancer cell of the cancerpatient that are longer than a first length but shorter than the lengthof the whole chromosome containing the LOH region, wherein the at leastone pair of human chromosomes is not a human X/Y sex chromosome pair,wherein the first length is about 1.5 or more megabases, and (b)identifying the patient as being likely to respond to the cancertreatment regimen.

In another aspect, this document features a method for assessing apatient. The method comprises, or consists essentially of, (a)determining that the patient comprises cancer cells having an LOHsignature, wherein the presence of more than a reference number of LOHregions in at least one pair of human chromosomes of a cancer cell ofthe cancer patient that are longer than a first length but shorter thanthe length of the whole chromosome containing the LOH region indicatesthat the cancer cells have the LOH signature, wherein the at least onepair of human chromosomes is not a human X/Y sex chromosome pair,wherein the first length is about 1.5 or more megabases, and (b)diagnosing the patient as having cancer cells with the LOH signature.

In another aspect, this document features a method for assessing apatient. The method comprises, or consists essentially of, (a)determining that the patient comprises cancer cells having an HDRdeficiency status, wherein the presence of more than a reference numberof LOH regions in at least one pair of human chromosomes of a cancercell of the cancer patient that are longer than a first length butshorter than the length of the whole chromosome containing the LOHregion indicates that the cancer cells have the HDR deficiency status,wherein the at least one pair of human chromosomes is not a human X/Ysex chromosome pair, wherein the first length is about 1.5 or moremegabases, and (b) diagnosing the patient as having cancer cells withthe HDR deficient status.

In another aspect, this document features a method for assessing apatient. The method comprises, or consists essentially of, (a)determining that the patient comprises cancer cells having a geneticmutation within a gene from an HDR pathway, wherein the presence of morethan a reference number of LOH regions in at least one pair of humanchromosomes of a cancer cell of the cancer patient that are longer thana first length but shorter than the length of the whole chromosomecontaining the LOH region indicates that the cancer cells have thegenetic mutation, wherein the at least one pair of human chromosomes isnot a human X/Y sex chromosome pair, wherein the first length is about1.5 or more megabases, and (b) diagnosing the patient as having cancercells with the genetic mutation.

In another aspect, this document features a method for assessing apatient for a likelihood to respond to a cancer treatment regimencomprising administering radiation or a drug selected from the groupconsisting of DNA damaging agents, anthracyclines, topoisomerase Iinhibitors, and PARP inhibitors. The method comprises, or consistsessentially of, (a) determining that the patient comprises cancer cellshaving an LOH signature, wherein the presence of more than a referencenumber of LOH regions in at least one pair of human chromosomes of acancer cell of the cancer patient that are longer than a first lengthbut shorter than the length of the whole chromosome containing the LOHregion indicates that the cancer cells have the LOH signature, whereinthe at least one pair of human chromosomes is not a human X/Y sexchromosome pair, wherein the first length is about 1.5 or moremegabases, and (b) diagnosing, based at least in part on the presence ofthe LOH signature, the patient as being likely to respond to the cancertreatment regimen.

In another aspect, this document features a method for performing adiagnostic analysis of a cancer cell of a patient. The method comprises,or consists essentially of, (a) detecting the presence of more than areference number of LOH regions in at least one pair of humanchromosomes of the cancer cell that are longer than a first length butshorter than the length of the whole chromosome containing the LOHregion, wherein the at least one pair of human chromosomes is not ahuman X/Y sex chromosome pair, wherein the first length is about 1.5 ormore megabases, and (b) identifying the patient as having cancer cellswith an LOH signature.

In another aspect, this document features a method for performing adiagnostic analysis of a cancer cell of a patient. The method comprises,or consists essentially of, (a) detecting the presence of more than areference number of LOH regions in at least one pair of humanchromosomes of the cancer cell that are longer than a first length butshorter than the length of the whole chromosome containing the LOHregion, wherein the at least one pair of human chromosomes is not ahuman X/Y sex chromosome pair, wherein the first length is about 1.5 ormore megabases, and (b) identifying the patient as having cancer cellswith a HDR deficient status.

In another aspect, this document features a method for performing adiagnostic analysis of a cancer cell of a patient. The method comprises,or consists essentially of, (a) detecting the presence of more than areference number of LOH regions in at least one pair of humanchromosomes of the cancer cell that are longer than a first length butshorter than the length of the whole chromosome containing the LOHregion, wherein the at least one pair of human chromosomes is not ahuman X/Y sex chromosome pair, wherein the first length is about 1.5 ormore megabases, and (b) identifying the patient as having cancer cellswith a genetic mutation within a gene from an HDR pathway.

In another aspect, this document features a method for performing adiagnostic analysis of a cancer cell of a patient to determine if thecancer patient is likely to respond to a cancer treatment regimencomprising administering radiation or a drug selected from the groupconsisting of DNA damaging agents, anthracyclines, topoisomerase Iinhibitors, and PARP inhibitors. The method comprises, or consistsessentially of, (a) detecting the presence of more than a referencenumber of LOH regions in at least one pair of human chromosomes of thecancer cell that are longer than a first length but shorter than thelength of the whole chromosome containing the LOH region, wherein the atleast one pair of human chromosomes is not a human X/Y sex chromosomepair, wherein the first length is about 1.5 or more megabases, and (b)identifying the patient as being likely to respond to the cancertreatment regimen.

In another aspect, this document features a method for diagnosing apatient as having cancer cells having an LOH signature. The methodcomprises, or consists essentially of, (a) determining that the patientcomprises cancer cells having the LOH signature, wherein the presence ofmore than a reference number of LOH regions in at least one pair ofhuman chromosomes of a cancer cell of the cancer patient that are longerthan a first length but shorter than the length of the whole chromosomecontaining the LOH region indicates that the cancer cells have the LOHsignature, wherein the at least one pair of human chromosomes is not ahuman X/Y sex chromosome pair, wherein the first length is about 1.5 ormore megabases, and (b) diagnosing the patient as having cancer cellswith the LOH signature.

In another aspect, this document features a method for diagnosing apatient as having cancer cells with an HDR deficient status. The methodcomprises, or consists essentially of, (a) determining that the patientcomprises cancer cells having the HDR deficiency status, wherein thepresence of more than a reference number of LOH regions in at least onepair of human chromosomes of a cancer cell of the cancer patient thatare longer than a first length but shorter than the length of the wholechromosome containing the LOH region indicates that the cancer cellshave the HDR deficiency status, wherein the at least one pair of humanchromosomes is not a human X/Y sex chromosome pair, wherein the firstlength is about 1.5 or more megabases, and (b) diagnosing the patient ashaving cancer cells with the HDR deficient status.

In another aspect, this document features a method for diagnosing apatient as having cancer cells with a genetic mutation within a genefrom an HDR pathway. The method comprises, or consists essentially of,(a) determining that the patient comprises cancer cells having thegenetic mutation, wherein the presence of more than a reference numberof LOH regions in at least one pair of human chromosomes of a cancercell of the cancer patient that are longer than a first length butshorter than the length of the whole chromosome containing the LOHregion indicates that the cancer cells have the genetic mutation,wherein the at least one pair of human chromosomes is not a human X/Ysex chromosome pair, wherein the first length is about 1.5 or moremegabases, and (b) diagnosing the patient as having cancer cells withthe genetic mutation.

In another aspect, this document features a method for diagnosing apatient as being a candidate for a cancer treatment regimen comprisingadministering radiation or a drug selected from the group consisting ofDNA damaging agents, anthracyclines, topoisomerase I inhibitors, andPARP inhibitors. The method comprises, or consists essentially of, (a)determining that the patient comprises cancer cells having an LOHsignature, wherein the presence of more than a reference number of LOHregions in at least one pair of human chromosomes of a cancer cell ofthe cancer patient that are longer than a first length but shorter thanthe length of the whole chromosome containing the LOH region indicatesthat the cancer cells have the LOH signature, wherein the at least onepair of human chromosomes is not a human X/Y sex chromosome pair,wherein the first length is about 1.5 or more megabases, and (b)diagnosing, based at least in part on the presence of the LOH signature,the patient as being likely to respond to the cancer treatment regimen.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used to practicethe invention, suitable methods and materials are described below. Allpublications, patent applications, patents, and other referencesmentioned herein are incorporated by reference in their entirety. Incase of conflict, the present specification, including definitions, willcontrol. In addition, the materials, methods, and examples areillustrative only and not intended to be limiting.

The details of one or more embodiments of the invention are set forth inthe accompanying drawings and the description below. Other features,objects, and advantages of the invention will be apparent from thedescription and drawings, and from the claims.

DESCRIPTION OF THE DRAWINGS

FIG. 1 is a graph plotting allele dosages of breast cancer cells from abreast cancer patient along chromosome 1 as determined using a SNParray. The arrow indicates a transition between a region ofheterozygosity and an LOH region.

FIG. 2 is a graph plotting allele dosages of breast cancer cells for thesame breast cancer patient as on FIG. 1 along chromosome 1 as determinedusing high-throughput sequencing. The arrow indicates a transitionbetween a region of heterozygosity and an LOH region.

FIG. 3 is a flow chart of an example process for assessing the genome ofa cell (e.g., a cancer cell) for an LOH signature.

FIG. 4 is a diagram of an example of a computer device and a mobilecomputer device that can be used to implement the techniques describedherein.

FIG. 5 is a graph plotting the length distribution of LOH regionsdetected in ovarian cancer cells from 62 human patients. The adjustedlength refers to the fraction of chromosomes arms covered by LOHregions.

FIG. 6 is a graph plotting the number of LOH regions longer than 15 Mband shorter than the entire chromosome for a training set of ovariancancer cell samples with intact or deficient BRCA1 and BRCA2 genes. Thesize of the circles is proportional to the number of samples with suchnumber of LOH regions.

FIG. 7 is a graph plotting the number of LOH regions longer than 15 Mband shorter than the entire chromosome for a training and validationsets of ovarian cancer cell samples with intact or deficient BRCA1 andBRCA2 genes. The size of the circles is proportional to the number ofsamples with such number of LOH regions.

FIG. 8 is a graph plotting the number of LOH regions longer than 15 Mband shorter than the entire chromosome for ovarian cancer cell sampleswith somatic BRCA mutations, with germline BRCA mutations, with lowBRCA1 expression, or with intact BRCA (BRCA normal). The size of thecircles is proportional to the number of samples with such number of LOHregions.

FIG. 9 is a table showing the percent of ovarian cancer samples that areBRCA deficient, HDR deficient/BRCA intact, and HDR intact.

FIG. 10 is a graph plotting the number of LOH regions longer than 15 Mband shorter than the entire chromosome for cancer cell lines for theindicated cancers. The size of the circles is proportional to the numberof samples with such number of LOH regions.

FIG. 11 is a graph plotting the number of LOH regions longer than 15 Mband shorter than the entire chromosome for lung cancer samples.

FIG. 12 is a graph plotting the percentage of the indicated cancers orcancer cell lines having an HDR deficiency.

FIG. 13 contains graphs plotting the IC₅₀ values (Log₁₀(IC₅₀) ofcamptothecin, as well as averaged Log₁₀(IC₅₀) values for platinumcompounds (oxaliplatin, cisplatin, and carboplatin), or anthracyclines(doxorubicin and epirubicin) when exposed to 29 breast cancer cell lineshaving the indicated number of LOH regions longer than 15 Mb and shorterthan the entire chromosome or the IC₅₀ values (Log₁₀(IC₅₀)) ofpaclitaxel when exposed to 27 ovarian cancer cell lines having theindicated number of LOH regions longer than 15 Mb and shorter than theentire chromosome. The dashed lines place a threshold number at nine.

FIG. 14 is a labeled version of a graph from FIG. 13 that plots theaveraged Log₁₀(IC₅₀) values of platinum compounds (oxaliplatin,cisplatin, and carboplatin) when exposed to 29 breast cancer cell lineshaving the indicated number of LOH regions longer than 15 Mb and shorterthan the entire chromosome.

FIG. 15 is a flow chart of an example computational process foridentifying LOH loci and regions.

DETAILED DESCRIPTION

This document provides methods and materials involved in assessingsamples (e.g., cancer cells) for the presence of an LOH signature. Forexample, this document provides methods and materials for determiningwhether or not a cell (e.g., a cancer cell) contains an LOH signature.

In general, a comparison of sequences present at the same locus on eachchromosome (each autosomal chromosome for males) can reveal whether thatparticular locus is homozygous or heterozygous within the genome of acell. Polymorphic loci within the human genome are generallyheterozygous within an individual since that individual typicallyreceives one copy from the biological father and one copy from thebiological mother. In some cases, a polymorphic locus or a string ofpolymorphic loci within an individual are homozygous as a result ininheriting identical copies from both biological parents.

Loss of heterozygosity (LOH) may result from several mechanisms. Forexample, in some cases, a region of one chromosome can be deleted in asomatic cell. The region that remains present on the other chromosome(the other non-sex chromosome for males) is an LOH region as there isonly one copy (instead of two copies) of that region present within thegenome of the affected cells. This LOH region can be any length (e.g.,from a length less than about 1.5 Mb up to a length equal to the entirelength of the chromosome). This type of LOH event results in a copynumber reduction. In other cases, a region of one chromosome (onenon-sex chromosome for males) in a somatic cell can be replaced with acopy of that region from the other chromosome, thereby eliminating anyheterozygosity that may have been present within the replaced region. Insuch cases, the region that remains present on each chromosome is an LOHregion and can be referred to as a copy neutral LOH region. Copy neutralLOH regions can be any length (e.g., from a length less than about 1.5Mb up to a length equal to the entire length of the chromosome).

As described herein, a cellular sample (e.g., cancer cell sample) can beidentified as having a positive LOH signature status if the genome ofthe cells being assessed contains five or more (e.g., six or more, sevenor more, eight or more, nine or more, ten or more, eleven or more, 12 ormore, 13 or more, 14 or more, 15 or more, 16 or more, 17 or more, 18 ormore, 19 or more, or 20 or more) LOH regions that are (a) longer thanabout 1.5 megabases (e.g., longer than about 2, 2.5, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50,75, or 100 megabases (Mb)) and (b) less than the length of the entirechromosome that contains that LOH region. In some cases, a cancer cellsample can be identified as having a positive LOH signature status ifthe genome of the cells being assessed contains nine or more LOH regionsthat are (a) longer than about 15 Mb and (b) less than the length of theentire chromosome that contains that LOH region. Unless otherwisedefined, the term “Indicator LOH Region” refers to an LOH region that isin a pair of human chromosomes other than the human X/Y sex chromosomepair, and that is characterized by loss of heterozygosity with a lengthof about 1.5 or more megabases but shorter than the length of the wholechromosome containing the LOH region. The length of the whole chromosomecontaining an LOH region may be determined by examining the length ofthe shorter chromosome of the corresponding chromosome pair in agermline cell or a non-tumor somatic cell. In some embodiments, anIndicator LOH Region is any LOH region about 2, 2.5, 3, 4, 5, 6, 7, 8,9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 25, 30, 35, 40, 45, 50,75, or 100 megabases (Mb)) or more and less than the length of the wholechromosome that contains that LOH region.

Cells (e.g., cancer cells) identified as having a positive LOH signaturestatus can be classified as having an increased likelihood of having anHDR deficiency and/or as having an increased likelihood of having adeficient status in one or more genes in the HDR pathway. For example,cancer cells identified as having a positive LOH signature status can beclassified as having an increased likelihood of having an HDR deficientstatus. In some cases, cancer cells identified as having a positive LOHsignature status can be classified as having an increased likelihood ofhaving a deficient status for one or more genes in the HDR pathway. Asused herein, deficient status for a gene means the sequence, structure,expression and/or activity of the gene or its product is/are deficientas compared to normal. Examples include, but are not limited to, low orno mRNA or protein expression, deleterious mutations, hypermethylation,attenuated activity (e.g., enzymatic activity, ability to bind toanother biomolecule), etc. As used herein, deficient status for apathway (e.g., HDR pathway) means at least one gene in that pathway(e.g., BRCA1) has a deficient status. Examples of highly deleteriousmutations include frameshift mutations, stop codon mutations, andmutations that lead to altered RNA splicing. Deficient status in a genein the HDR pathway may result in deficiency or reduced activity inhomology directed repair in the cancer cells. Examples of genes in theHDR pathway include, without limitation, the genes listed in Table 1.

TABLE 1 Selected HDR Pathway Genes Entrez Gene Symbol Gene Name (ifdifferent) Entrez Gene Id BLM BLM 641 BRCA1 BRCA1 672 BRCA2 BRCA2 675CtIP RBBP8 5932 DNA polymerase delta POLD1 5424 POLD2 5424 POLD3 10714POLD4 57804 DNA polymerase eta POLH 5429 DNA2 DNA2 1763 EME1 EME1 146956ERCC1 ERCC1 2067 EXO1 EXO1 9156 FANCM FANCM 57697 GEN1 GEN1 348654 MRE11MRE11A 4361 MUS81 MUS81 80198 NBS1 NBN 4683 PAEB2 PALB2 79728 PCNA PCNA5111 RAD50 RAD50 10111 RAD51 RAD51 5888 RAD51AP1 RAD51AP1 10635 RAD51BRAD51L1 5890 RAD51C RAD51C 5889 RAD51D RAD51L3 5892 RAD54 ATRX 546RAD54B RAD54B 25788 RMI1 RMI1 80010 RMI2 C16orf75 116028 RPA RPA1 6117RTEL1 RTEL1 51750 SLX1 SLX2 SLX4 SLX4 84464 TOP2A TOP2A 7153 XPF ERCC42072 XRCC2 XRCC2 7516 XRCC3 XRCC3 7517

Examples of genetic mutations that can be present within a gene of theHDR pathway include, without limitation, those listed in Table 2.

TABLE 2 Possible genetic mutations within selected genes of the HDRpathway. Gene Mutation Entrez Gene ID BRCA1 C24F 672 BRCA1 E29X 672BRCA2 R3052W 675 BRCA2 2881delG 675 RAD51C G125V 5889 RAD51C L138F 5889RAD51C Y75XfsX0 5889

In some cases, a cellular sample (e.g., cancer cell sample) can beidentified as having an increased number of LOH regions (e.g., at least7, 8, 9, 10, or more LOH regions) that cover the whole chromosome. Cells(e.g., cancer cells) identified as having an increased number of LOHregions that cover the whole chromosome can be classified as having anincreased likelihood of having intact genes in the HDR pathway. Forexample, cancer cells identified as having an increased number of LOHregions that cover the whole chromosome can be classified as being morelikely to have intact BRCA1 and BRCA2 genes.

As described herein, identifying LOH loci (as well as the size andnumber of LOH regions) can include, first, determining the genotype of asample at various genomic loci (e.g., SNP loci, individual bases inlarge sequencing) and, second, determining whether homozygous loci aredue to LOH events. Any appropriate technique can be used to determinegenotypes at loci of interest within the genome of a cell. For example,single nucleotide polymorphisms (SNP) arrays (e.g., human genome-wideSNP arrays), targeted sequencing of loci of interest (e.g., sequencingSNP loci and their surrounding sequences), and even untargetedsequencing (e.g., whole exome, transcriptome, or genome sequencing) canbe used to identify loci as being homozygous or heterozygous. In somecases, an analysis of the homozygous or heterozygous nature of loci overa length of a chromosome can be performed to determine the length ofregions of homozygosity or heterozygosity. For example, a stretch of SNPlocations that are spaced apart (e.g., spaced about 25 kb to about 100kb apart) along a chromosome can be evaluated using SNP array results todetermine not only the presence of a region of homozygosity along achromosome but also the length of that region. Results from a SNP arraycan be used to generate a graph that plots allele dosages along achromosome. Allele dosage d_(i) for SNP i can be calculated fromadjusted signal intensities of two alleles (A_(i) and B_(i)):d_(i)=A_(i)/(A_(i)+B_(i)). An example of such a graph is presented inFIG. 1.

Once a sample's genotype has been determined for a plurality of loci(e.g., SNPs), common techniques can be used to identify loci and regionsof LOH. One way to determine whether homozygosity is due to LOH is tocompare the somatic genotype to the germline. For example, the genotypefor a plurality of loci (e.g., SNPs) can be determined in both agermline (e.g., blood) sample and a somatic (e.g., tumor) sample. Thegenotypes for each sample can be compared (typically computationally) todetermine where the genome of the germline cell was heterozygous and thegenome of the somatic cell is homozygous. Such loci are LOH loci andregions of such loci are LOH regions.

Computational techniques can also be used to determine whetherhomozygosity is due to LOH. Such techniques are particularly useful whena germline sample is not available for analysis and comparison. Forexample, algorithms such as those described elsewhere can be used todetect LOH regions using information from SNP arrays (Nannya et al.,CANCER RES. (2005) 65:6071-6079). Typically these algorithms do notexplicitly take into account contamination of tumor samples with benigntissue. Cf. International Application No. PCT/US2011/026098 to Abkevishet al.; Goransson et al., PLoS ONE (2009) 4(6):e6057. This contaminationis often high enough to make the detection of LOH regions challenging.Improved analytical methods according to the present invention foridentifying LOH, even in spite of contamination, include those embodiedin computer software products as described below.

The following is one example. If the observed ratio of the signals oftwo alleles, A and B, is two to one, there are two possibilities. Thefirst possibility is that cancer cells have LOH with deletion of alleleB in a sample with 50% contamination with normal cells. The secondpossibility is that there is no LOH but allele A is duplicated in asample with no contamination with normal cells. An algorithm can beimplemented as a computer program as described herein to reconstruct LOHregions based on genotype (e.g., SNP genotype) data. One point of thealgorithm is to first reconstruct allele specific copy numbers (ASCN) ateach locus (e.g., SNP). ASCNs are the numbers of copies of both paternaland maternal alleles. An LOH region is then determined as a stretch ofSNPs with one of the ASCNs (paternal or maternal) being zero. Thealgorithm can be based on maximizing a likelihood function and can beconceptually akin to a previously described algorithm designed toreconstruct total copy number (rather than ASCN) at each locus (e.g.,SNP). See International Application No. PCT/US2011/026098 to Abkevish etal. The likelihood function can be maximized over ASCN of all loci,level of contamination with benign tissue, total copy number averagedover the whole genome, and sample specific noise level. The input datafor the algorithm can include or consist of (1) sample-specificnormalized signal intensities for both allele of each locus and (2)assay-specific (specific for different SNP arrays and for sequence basedapproach) set of parameters defined based on analysis of large number ofsamples with known ASCN profiles.

In some cases, nucleic acid sequencing techniques can be used toidentify loci as being homozygous or heterozygous. For example, genomicDNA from a cell sample (e.g., a cancer cell sample) can be extracted andfragmented. Any appropriate method can be used to extract and fragmentgenomic nucleic acid including, without limitation, commercial kits suchas QlAamp DNA Mini Kit (Qiagen), MagNA Pure DNA Isolation Kit (RocheApplied Science) and GenElute Mammalian Genomic DNA Miniprep Kit(Sigma-Aldrich). Once extracted and fragmented, either targeted oruntargeted sequencing can be done to determine the sample's genotypes atloci. For example, whole genome, whole transcriptome, or whole exomesequencing can be done to determine genotypes at millions or evenbillions of base pairs (i.e., base pairs can be “loci” to be evaluated).

In some cases, targeted sequencing of known polymorphic loci (e.g., SNPsand surrounding sequences) can be done as an alternative to microarrayanalysis. For example, the genomic DNA can be enriched for thosefragments containing a locus (e.g., SNP location) to be analyzed usingkits designed for this purpose (e.g., Agilent SureSelect, IlluminaTruSeq Capture, and Nimblegen SeqCap EZ Choice). For example, genomicDNA containing the loci to be analyzed can be hybridized to biotinylatedcapture RNA fragments to form biotinylated RNA/genomic DNA complexes.Alternatively, DNA capture probes may be utilized resulting in theformation of biotinylated DNA/genomic DNA hybrids. Streptavidin coatedmagnetic beads and a magnetic force can be used to separate thebiotinylated RNA/genomic DNA complexes from those genomic DNA fragmentsnot present within a biotinylated RNA/genomic DNA complex. The obtainedbiotinylated RNA/genomic DNA complexes can be treated to remove thecaptured RNA from the magnetic beads, thereby leaving intact genomic DNAfragments containing a locus to be analyzed. These intact genomic DNAfragments containing the loci to be analyzed can be amplified using, forexample, PCR techniques. The amplified genomic DNA fragments can besequenced using a high-throughput sequencing technology or anext-generation sequencing technology such as Illumina HiSeq, IlluminaMiSeq, Life Technologies SoLID, or Roche's 454.

The sequencing results from the genomic DNA fragments can be used toidentify loci as being homozygous or heterozygous, analogous to themicroarray analysis described herein. In some cases, an analysis of thehomozygous or heterozygous nature of loci over a length of a chromosomecan be performed to determine the length of regions of homozygosity orheterozygosity. For example, a stretch of SNP locations that are spacedapart (e.g., spaced about 25 kb to about 100 kb apart) along achromosome can be evaluated by sequencing, and the sequencing resultsused to determine not only the presence of a region of homozygosityalong a chromosome but also the length of that LOH region. Obtainedsequencing results can be used to generate a graph that plots alleledosages along a chromosome. Allele dosage d_(i) for SNP i can becalculated from adjusted number of captured probes for two alleles(A_(i) and B_(i)): d_(i)=A_(i)/(A_(i)+B_(i)). An example of such a graphis presented in FIG. 2. Determining whether homozygosity is due to LOH(as opposed to homozygosity in the germline) can be performed asdescribed herein.

In some cases, a selection process can be used to select loci (e.g., SNPloci) to be evaluated using an assay configured to identify loci asbeing homozygous or heterozygous (e.g., SNP array-based assays andsequencing-based assays). For example, any human SNP location can beselected for inclusion in a SNP array-based assay or a sequencing-basedassay configured to identify loci as being homozygous or heterozygouswithin the genome of cells. In some cases, 0.5, 1.0, 1.5, 2.0, 2.5million or more SNP locations present within the human genome can beevaluated to identify those SNPs that (a) are not present on the Ychromosome, (b) are not mitochondrial SNPs, (c) have a minor allelefrequency of at least about five percent in Caucasians, (d) have a minorallele frequency of at least about one percent in three races other thanCaucasians (e.g., Chinese, Japanese, and Yoruba), and/or (e) do not havea significant deviation from Hardy Weinberg equilibrium in any of thefour races. In some cases, more than 100,000, 150,000, or 200,000 humanSNPs can be selected that meet criteria (a) through (e). Of the humanSNPs meeting criteria (a) through (e), a group of SNPs (e.g., top110,000 SNPs) can be selected such that the SNPs have a high degree ofallele frequency in Caucasians, cover the human genome in a somewhatevenly spaced manner (e.g., at least one SNP every about 25 kb to about500 kb), and are not in linkage disequilibrium with another selected SNPfor in any of the four races. In some cases, about 40, 50, 60, 70, 80,90, 100, 110, 120, 130 thousand or more SNPs can be selected as meetingeach of these criteria and included in an assay configured to identifyLOH regions across a human genome. For example, between about 70,000 andabout 90,000 (e.g., about 80,000) SNPs can be selected for analysis witha SNP array-based assay, and between about 45,000 and about 55,000(e.g., about 54,000) SNPs can be selected for analysis with asequencing-based assay.

As described herein, a cell sample can be assessed to determine if thegenome of cells of the sample contains an LOH signature, lacks an LOHsignature, has an increased number of LOH regions that cover the wholechromosome, or lacks an increased number of LOH regions that cover thewhole chromosome. Any appropriate type of sample can be assessed. Forexample, a sample containing cancer cells can be assessed to determineif the genome of the cancer cells contains an LOH signature, lacks anLOH signature, has an increased number of LOH regions that cover thewhole chromosome, or lacks an increased number of LOH regions that coverthe whole chromosome. Examples of samples containing cancer cells thatcan be assessed as described herein include, without limitation, tumorbiopsy samples (e.g., breast tumor biopsy samples), formalin-fixed,paraffin-embedded tissue samples containing cancer cells, core needlebiopsies, fine needle aspirates, and samples containing cancer cellsshed from a tumor (e.g., blood, urine or other bodily fluids). Forformalin-fixed, paraffin-embedded tissue samples, the sample can beprepared by DNA extraction using a genomic DNA extraction kit optimizedfor FFPE tissue, including but not limited to those described above(e.g., QuickExtract FFPE DNA Extraction Kit (Epicentre), and QlAamp DNAFFPE Tissue Kit (Qiagen)).

In some cases, laser dissection techniques can be performed on a tissuesample to minimize the number of non-cancer cells within a cancer cellsample to be assessed. In some cases, antibody based purificationmethods can be used to enrich for cancer cells and/or deplete non-cancercells. Examples of antibodies that could be used for cancer cellenrichment include, without limitation, anti-EpCAM, anti-TROP-2,anti-c-Met, anti-Folate binding protein, anti-N-Cadherin, anti-CD318,anti-antimesencymal stem cell antigen, anti-Her2, anti-MUC1, anti-EGFR,anti-cytokeratins (e.g., cytokeratin 7, cytokeratin 20, etc.),anti-Caveolin-1, anti-PSA, anti-CA125, and anti-surfactant proteinantibodies.

Any type of cancer cell can be assessed using the methods and materialsdescribed herein. For example, breast cancer cells, ovarian cancercells, liver cancer cells, esophageal cancer cells, lung cancer cells,head and neck cancer cells, prostate cancer cells, colon, rectal, orcolorectal cancer cells, and pancreatic cancer cells can be assessed todetermine if the genome of the cancer cells contains an LOH signature,lacks an LOH signature, has an increased number of LOH regions thatcover the whole chromosome, or lacks an increased number of LOH regionsthat cover the whole chromosome.

When assessing the genome of cancer cells for the presence or absence ofan LOH signature, one or more (e.g., one, two, three, four, five, six,seven, eight, nine, ten, eleven, twelve, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, or 23) pairs of chromosomes can be assessed. In some cases, thegenome of cancer cells is assessed for the presence or absence of an LOHsignature using one or more (e.g., one, two, three, four, five, six,seven, eight, nine, ten, eleven, twelve, 13, 14, 15, 16, 17, 18, 19, 20,21, 22, 23) pairs of chromosomes.

In some cases, it can be helpful to exclude certain chromosomes fromthis analysis. For example, in the case of females, a pair to beassessed can include the pair of X sex chromosomes; whereas, in the caseof males, a pair of any autosomal chromosomes (i.e., any pair other thanthe pair of X and Y sex chromosomes) can be assessed. As anotherexample, in some cases the chromosome number 17 pair may be excludedfrom the analysis. It has been determined that certain chromosomes carryunusually high levels of LOH in certain cancers and, thus, it can behelpful to exclude such chromosomes when analyzing samples as describedherein from patients having these cancers. In some cases, the sample isfrom a patient having ovarian cancer, and the chromosome to be excludedis chromosome 17.

When assessing the genome of cancer cells for the presence or absence ofan increased number of LOH regions that cover the whole chromosome, 10or more (e.g., 13, 16, 19 or 23) pairs of chromosomes can be assessed.In the case of females, a pair to be assessed can include the pair of Xsex chromosomes; whereas, in the case of males, a pair of any autosomalchromosomes (i.e., any pair other than the pair of X and Y sexchromosomes) can be assessed. In some cases, the chromosome number 17pair may be excluded from the analysis. In some cases, the sample isfrom a patient having ovarian cancer, and the chromosome to be excludedis chromosome 17. In some cases, the genome of cancer cells is assessedfor the presence or absence of an increased number of LOH regions thatcover the whole chromosome using 10 or more (e.g., 13, 16 19, or 23)pairs of chromosomes.

As described herein, patients having cancer cells identified as having apositive LOH signature status can be classified, based at least in parton a positive LOH signature status, as being likely to respond to aparticular cancer treatment regimen. For example, patients having cancercells with a genome containing an LOH signature can be classified, basedat least in part on a positive LOH signature status, as being likely torespond to a cancer treatment regimen that includes the use of a DNAdamaging agent, a PARP inhibitor, radiation, or a combination thereof.Examples of DNA damaging agents include, without limitation,platinum-based chemotherapy drugs (e.g., cisplatin, carboplatin,oxaliplatin, and picoplatin), anthracyclines (e.g., epirubicin anddoxorubicin), topoisomerase I inhibitors (e.g., campothecin, topotecan,and irinotecan), and triazene compounds (e.g., dacarbazine andtemozolomide). Examples of PARP inhibitors include, without limitation,olaparib, iniparib, and veliparib. Examples of information that can beused in addition to a positive LOH signature status to base aclassification of being likely to respond to a particular cancertreatment regimen include, without limitation, previous treatmentresults, germline or somatic DNA mutations, gene or protein expressionprofiling (e.g., ER/PR/HER2 status, PSA levels), tumor histology (e.g.,adenocarcinoma, squamous cell carcinoma, papillary serous carcinoma,mucinous carcinoma, invasive ductal carcinoma, ductal carcinoma insitu(non-invasive), etc.), disease stage, tumor or cancer grade (e.g., well,moderately, or poorly differentiated (e.g., Gleason, modified BloomRichardson), etc.), number of previous courses of treatment, etc.

Once classified as being likely to respond to a particular cancertreatment regimen (e.g., a cancer treatment regimen that includes theuse of a DNA damaging agent, a PARP inhibitor, radiation, or acombination thereof), the cancer patient can be treated with such acancer treatment regimen. Any appropriate method for treating the cancerat issue can be used to treat a cancer patient identified as havingcancer cells having a positive LOH signature status. For example,platinum-based chemotherapy drugs or a combination of platinum-basedchemotherapy drugs can be used to treat cancer as described elsewhere(see, e.g., U.S. Pat. Nos. 3,892,790, 3,904,663, 7,759,510, 7,759,488and 7,754,684. In some cases, anthracyclines or a combination ofanthracyclines can be used to treat cancer as described elsewhere (see,e.g., U.S. Pat. Nos. 3,590,028, 4,138,480, 4,950,738, 6,087,340,7,868,040, and 7,485,707. In some cases, topoisomerase I inhibitors or acombination of topoisomerase I inhibitors can be used to treat cancer asdescribed elsewhere (see, e.g., U.S. Pat. Nos. 5,633,016 and 6,403,563.In some cases, PARP inhibitors or a combination of PARP inhibitors canbe used to treat cancer as described elsewhere (see, e.g., U.S. Pat.Nos. 5,177,075, 7,915,280, and 7,351,701. In some cases, radiation canbe used to treat cancer as described elsewhere (see, e.g., U.S. Pat. No.5,295,944). In some cases, a combination comprising different agents(e.g., a combination comprising any of platinum-based chemotherapydrugs, anthracyclines, topoisomerase I inhibitors, and/or PARPinhibitors) with or without radiation treatments can be used to treatcancer. In some cases, a combination treatment may comprise any of theabove agents or treatments (e.g., a DNA damaging agent, a PARPinhibitor, radiation, or a combination thereof) together with anotheragent or treatment—e.g., a taxane agent (e.g., doxetaxel, paclitaxel,abraxane), a growth factor or growth factor receptor inhibitor (e.g.,erlotinib, gefitinib, lapatinib, sunitinib, bevacizumab, cetuximab,trastuzumab, panitumumab), and/or an antimetabolite (e.g.,5-flourouracil, methotrexate).

In some cases, patients identified as having cancer cells with a genomelacking an LOH signature can be classified, based at least in part on anegative LOH signature status, as being less likely to respond to atreatment regimen that includes a DNA damaging agent, a PARP inhibitor,radiation, or a combination thereof. In turn, such a patient can beclassified as likely to respond to a cancer treatment regimen thatincludes the use of one or more cancer treatment agents not associatedwith HDR, such as a taxane agent (e.g., doxetaxel, paclitaxel,abraxane), a growth factor or growth factor receptor inhibitor (e.g.,erlotinib, gefitinib, lapatinib, sunitinib, bevacizumab, cetuximab,trastuzumab, panitumumab), and/or an antimetabolite agent (e.g.,5-flourouracil, methotrexate). Once classified as being likely torespond to a particular cancer treatment regimen (e.g., a cancertreatment regimen that includes the use of a cancer treatment agent notassociated with HDR), the cancer patient can be treated with such acancer treatment regimen. Any appropriate method for the cancer beingtreated can be used to treat a cancer patient identified as havingcancer cells having a negative LOH signature status. Examples ofinformation that can be used in addition to a negative LOH signaturestatus to base a classification of being likely to respond to aparticular cancer treatment regimen include, without limitation,previous treatment results, germline or somatic DNA mutations, gene orprotein expression profiling (e.g., ER/PR/HER2 status, PSA levels),tumor histology (e.g., adenocarcinoma, squamous cell carcinoma,papillary serous carcinoma, mucinous carcinoma, invasive ductalcarcinoma, ductal carcinoma in situ (non-invasive), etc.), diseasestage, tumor or cancer grade (e.g., well, moderately, or poorlydifferentiated (e.g., Gleason, modified Bloom Richardson), etc.), numberof previous courses of treatment, etc.

Once treated for a particular period of time (e.g., between one to sixmonths), the patient can be assessed to determine whether or not thetreatment regimen has an effect. If a beneficial effect is detected, thepatient can continue with the same or a similar cancer treatmentregimen. If a minimal or no beneficial effect is detected, thenadjustments to the cancer treatment regimen can be made. For example,the dose, frequency of administration, or duration of treatment can beincreased. In some cases, additional anti-cancer agents can be added tothe treatment regimen or a particular anti-cancer agent can be replacedwith one or more different anti-cancer agents. The patient being treatedcan continue to be monitored as appropriate, and changes can be made tothe cancer treatment regimen as appropriate.

As described herein, this document provides methods for assessingpatients for cells (e.g., cancer cells) having a genome containing anLOH signature. For example, one or more clinicians or medicalprofessionals can determine if a patient contains cancer cells having agenome containing an LOH signature. In some cases, one or moreclinicians or medical professionals can determine if a patient containscancer cells having a genome containing an LOH signature by obtaining acancer cell sample from the patient and assessing the genome of cancercells of the cancer cell sample to determine the presence or absence ofan LOH signature as described herein.

In some cases, one or more clinicians or medical professionals canobtain a cancer cell sample from a patient and provide that sample to atesting laboratory having the ability to assess the genome of cancercells of the cancer cell sample to provide an indication about thepresence or absence of an LOH signature as described herein. In suchcases, the one or more clinicians or medical professionals can determineif a patient contains cancer cells having a genome containing an LOHsignature by receiving information about the presence or absence of anLOH signature directly or indirectly from the testing laboratory. Forexample, a testing laboratory, after assessing the genome of cancercells for presence or absence of an LOH signature as described herein,can provide a clinician or medical professional with, or access to, awritten, electronic, or oral report or medical record that provides anindication about the presence or absence of an LOH signature for aparticular patient being assessed. Such a written, electronic, or oralreport or medical record can allow the one or more clinicians or medicalprofessionals to determine if a particular patient being assessedcontains cancer cells having a genome containing an LOH signature.

Once a clinician or medical professional or group of clinicians ormedical professionals determines that a particular patient beingassessed contains cancer cells having a genome containing an LOHsignature, the clinician or medical professional (or group) can classifythat patient as having cancer cells whose genome contains the presenceof an LOH signature. In some cases, a clinician or medical professionalor group of clinicians or medical professionals can diagnose a patientdetermined to have cancer cells whose genome contains the presence of anLOH signature as having cancer cells likely to be deficient in HDR. Sucha diagnosis can be based solely on a determination that a particularpatient being assessed contains cancer cells having a genome containingan LOH signature or can be based at least in part on a determinationthat a particular patient being assessed contains cancer cells having agenome containing an LOH signature. For example, a patient determined tohave cancer cells whose genome contains the presence of an LOH signaturecan be diagnosed as likely to be deficient in HDR based on thecombination of a positive LOH signature status and deficient status inone or more tumor suppressor genes (e.g., BRCA1/2, RAD51), a familyhistory of cancer, or the presence of behavioral risk factors (e.g.,smoking).

In some cases, a clinician or medical professional or group ofclinicians or medical professionals can diagnose a patient determined tohave cancer cells whose genome contains the presence of an LOH signatureas having cancer cells likely to contain genetic mutations in one ormore genes in the HDR pathway. Such a diagnosis can be based solely on adetermination that a particular patient being assessed contains cancercells having a genome containing an LOH signature or can be based atleast in part on a determination that a particular patient beingassessed contains cancer cells having a genome containing an LOHsignature. For example, a patient determined to have cancer cells whosegenome contains the presence of an LOH signature can be diagnosed ashaving cancer cells likely to contain genetic mutations in one or moregenes in the HDR pathway based on the combination of a positive LOHpositive status and a family history of cancer, or the presence ofbehavioral risk factors (e.g., smoking).

In some cases, a clinician or medical professional or group ofclinicians or medical professionals can diagnose a patient determined tohave cancer cells whose genome contains the presence of an LOH signatureas having cancer cells likely to respond to a particular cancertreatment regimen. Such a diagnosis can be based solely on adetermination that a particular patient being assessed contains cancercells having a genome containing an LOH signature or can be based atleast in part on a determination that a particular patient beingassessed contains cancer cells having a genome containing an LOHsignature. For example, a patient determined to have cancer cells whosegenome contains the presence of an LOH signature can be diagnosed asbeing likely to respond to a particular cancer treatment regimen basedon the combination of a positive LOH signature status and deficientstatus in one or more tumor suppressor genes (e.g., BRCA1/2, RAD51), afamily history of cancer, or the presence of behavioral risk factors(e.g., smoking). As described herein, a patient determined to havecancer cells whose genome contains the presence of an LOH signature canbe diagnosed as likely to respond to a cancer treatment regimen thatincludes the use of a platinum-based chemotherapy drug such ascisplatin, carboplatin, oxaliplatin, or picoplatin, an anthracyclinesuch as epirubicin or doxorubicin, a topoisomerase I inhibitor such ascampothecin, topotecan, or irinotecan, a PARP inhibitor, radiation, acombination thereof, or a combination of any of the preceding withanother anti-cancer agent.

Once a clinician or medical professional or group of clinicians ormedical professionals determines that a particular patient beingassessed contains cancer cells having a genome lacking an LOH signature,the clinician or medical professional (or group) can classify thatpatient as having cancer cells whose genome contains an absence of anLOH signature. In some cases, a clinician or medical professional orgroup of clinicians or medical professionals can diagnose a patientdetermined to have cancer cells containing a genome that lacks thepresence of an LOH signature as having cancer cells likely to havefunctional HDR. In some cases, a clinician or medical professional orgroup of clinicians or medical professionals can diagnose a patientdetermined to have cancer cells containing a genome that lacks thepresence of an LOH signature as having cancer cells that do not likelycontain genetic mutations in one or more genes in the HDR pathway. Insome cases, a clinician or medical professional or group of cliniciansor medical professionals can diagnose a patient determined to havecancer cells containing a genome that lacks the presence of an LOHsignature or contains an increased number of LOH regions that cover thewhole chromosome as having cancer cells that are less likely to respondto a platinum-based chemotherapy drug such as cisplatin, carboplatin,oxalaplatin, or picoplatin, an anthracycline such as epirubincin ordoxorubicin, a topoisomerase I inhibitor such as campothecin, topotecan,or irinotecan, a PARP inhibitor, or radiation and/or more likely torespond to a cancer treatment regimen that includes the use of a cancertreatment agent not associated with HDR such as one or more taxaneagents, growth factor or growth factor receptor inhibitors,anti-metabolite agents, etc.

As described herein, this document also provides methods for performinga diagnostic analysis of a nucleic acid sample (e.g., a genomic nucleicacid sample or amplified genomic nucleic acid sample) of a cancerpatient to determine if cancer cells within the patient have a genomecontaining an LOH signature and/or an increased number of LOH regionsthat cover the whole chromosome. For example, one or more laboratorytechnicians or laboratory professionals can detect the presence orabsence of an LOH signature in the genome of cancer cells of the patientor the presence or absence of an increased number of LOH regions thatcover the whole chromosome in the genome of cancer cells of the patient.In some cases, one or more laboratory technicians or laboratoryprofessionals can detect the presence or absence of an LOH signature orthe presence or absence of an increased number of LOH regions that coverthe whole chromosome in the genome of cancer cells of the patient by (a)receiving a cancer cell sample obtained from the patient, receiving agenomic nucleic acid sample obtained from cancer cells obtained from thepatient, or receiving an enriched and/or amplified genomic nucleic acidsample obtained from cancer cells obtained from the patient and (b)performing an analysis (e.g., a SNP array-based assay or asequencing-based assay) using the received material to detect thepresence or absence of an LOH signature or the presence or absence of anincreased number of LOH regions that cover the whole chromosome asdescribed herein. In some cases, one or more laboratory technicians orlaboratory professionals can receive a sample to be analyzed (e.g., acancer cell sample obtained from the patient, a genomic nucleic acidsample obtained from cancer cells obtained from the patient, or anenriched and/or amplified genomic nucleic acid sample obtained fromcancer cells obtained from the patient) directly or indirectly from aclinician or medical professional.

Once a laboratory technician or laboratory professional or group oflaboratory technicians or laboratory professionals detects the presenceof an LOH signature as described herein, the laboratory technician orlaboratory professional (or group) can identify the patient whose cancercells were detected as having an LOH signature as having cancer cellswith a positive LOH signature status. For example, one or morelaboratory technicians or laboratory professionals can identify apatient having cancer cells that were detected to have an LOH signatureas having cancer cells with a positive LOH signature status byassociating that positive LOH signature status or the result (or resultsor a summary of results) of the performed diagnostic analysis with thecorresponding patient's name, medical record, symbolic/numericalidentifier, or a combination thereof. In some cases, a laboratorytechnician or laboratory professional or group of laboratory techniciansor laboratory professionals can identify a patient having cancer cellsthat were detected to have an LOH signature as having cancer cellspotentially deficient in HDR by associating the positive LOH signaturestatus, the potentially deficient in HDR status, or the result (orresults or a summary of results) of the performed diagnostic analysiswith the corresponding patient's name, medical record,symbolic/numerical identifier, or a combination thereof. Suchidentification can be based solely on detecting the presence of an LOHsignature or can be based at least in part on detecting the presence ofan LOH signature. For example, a laboratory technician or laboratoryprofessional can identify a patient having cancer cells that weredetected to have an LOH signature as having cancer cells potentiallydeficient in HDR based on a combination of a positive LOH signaturestatus and the results of other genetic and biochemical tests performedat the testing laboratory.

In some cases, a laboratory technician or laboratory professional orgroup of laboratory technicians or laboratory professionals can identifya patient having cancer cells that were detected to have an LOHsignature as having cancer cells potentially containing a geneticmutation in one or more genes in the HDR pathway by associating thepositive LOH signature status, the potential presence of a geneticmutation in one or more genes in the HDR pathway, or the result (orresults or a summary of results) of the performed diagnostic analysiswith the corresponding patient's name, medical record,symbolic/numerical identifier, or a combination thereof. Suchidentification can be based solely on detecting the presence of an LOHsignature or can be based at least in part on detecting the presence ofan LOH signature. For example, a laboratory technician or laboratoryprofessional can identify a patient having cancer cells that weredetected to have an LOH signature as having cancer cells potentiallycontaining a genetic mutation in one or more genes in the HDR pathwaybased on a combination of a positive LOH signature status and theresults of other genetic and biochemical tests performed at the testinglaboratory.

In some cases, a laboratory technician or laboratory professional orgroup of laboratory technicians or laboratory professionals can identifya patient having cancer cells that were detected to have an LOHsignature as having cancer cells likely to respond to a particularcancer treatment regimen by associating the positive LOH signaturestatus, a potentially deficient HDR status, a potential presence of adeficient status in one or more genes in the HDR pathway, or the result(or results or a summary of results) of the performed diagnosticanalysis with the corresponding patient's name, medical record,symbolic/numerical identifier, or a combination thereof. Suchidentification can be based solely on detecting the presence of an LOHsignature or can be based at least in part on detecting the presence ofan LOH signature. For example, a laboratory technician or laboratoryprofessional can identify a patient having cancer cells that weredetected to have an LOH signature as having cancer cells likely torespond to a particular cancer treatment regimen based on a combinationof a positive LOH signature status and the results of other genetic andbiochemical tests performed at the testing laboratory.

Once a laboratory technician or laboratory professional or group oflaboratory technicians or laboratory professionals detects the absenceof an LOH signature, the laboratory technician or laboratoryprofessional (or group) can identify the patient whose cancer cells weredetected as lacking an LOH signature as having cancer cells with anegative LOH signature status. For example, one or more laboratorytechnicians or laboratory professionals can identify a patient havingcancer cells that were detected to lack an LOH signature as havingcancer cells with a negative LOH signature status by associating thatnegative LOH signature status or the result (or results or a summary ofresults) of the performed diagnostic analysis with the correspondingpatient's name, medical record, symbolic/numerical identifier, or acombination thereof. In some cases, a laboratory technician orlaboratory professional or group of laboratory technicians or laboratoryprofessionals can identify a patient having cancer cells that weredetected to lack an LOH signature as having cancer cells withpotentially intact HDR by associating the negative LOH signature status,the potentially intact HDR status, or the result (or results or asummary of results) of the performed diagnostic analysis with thecorresponding patient's name, medical record, symbolic/numericalidentifier, or a combination thereof.

In some cases, a laboratory technician or laboratory professional orgroup of laboratory technicians or laboratory professionals can identifya patient having cancer cells that were detected to lack an LOHsignature as having cancer cells with potentially intact genes of theHDR pathway by associating the negative LOH signature status, thepotential absence of genetic mutations in genes of the HDR pathway, orthe result (or results or a summary of results) of the performeddiagnostic analysis with the corresponding patient's name, medicalrecord, symbolic/numerical identifier, or a combination thereof.

In some cases, a laboratory technician or laboratory professional orgroup of laboratory technicians or laboratory professionals can identifya patient having cancer cells that were detected to lack an LOHsignature as having cancer cells as less likely to respond to oneparticular treatment (e.g., a platinum-based chemotherapy drug such ascisplatin, carboplatin, oxalaplatin, or picoplatin, an anthracyclinesuch as epirubincin or doxorubicin, a topoisomerase I inhibitor such ascampothecin, topotecan, or irinotecan, a PARP inhibitor such asiniparib, olaparib, or velapirib, or radiation) and/or more likely torespond to a particular cancer treatment regimen (e.g., a cancertreatment regimen that includes the use of a cancer treatment agent notassociated with HDR) by associating the negative LOH signature status, apotentially intact HDR status, a potential absence of genetic mutationsin genes of the HDR pathway, or the result (or results or a summary ofresults) of the performed diagnostic analysis with the correspondingpatient's name, medical record, symbolic/numerical identifier, or acombination thereof.

Once a laboratory technician or laboratory professional or group oflaboratory technicians or laboratory professionals detects the presenceof an increased number of LOH regions that cover the whole chromosome,the laboratory technician or laboratory professional (or group) canidentify the patient whose cancer cells were detected as having anincreased number of LOH regions that cover the whole chromosome aslikely having cancer cells with an intact BRCA1 and BRCA2 status. Forexample, one or more laboratory technicians or laboratory professionalscan identify a patient having cancer cells that were detected to have anincreased number of LOH regions that cover the whole chromosome aslikely having cancer cells with an intact BRCA1 and BRCA2 status byassociating the presence of an increased number of LOH regions thatcover the whole chromosome or the result (or results or a summary ofresults) of the performed diagnostic analysis with the correspondingpatient's name, medical record, symbolic/numerical identifier, or acombination thereof.

FIG. 15 shows an exemplary process by which a computing system (or acomputer program (e.g., software) containing computer-executableinstructions) can identify LOH loci or regions from genotype data asdescribed herein. If the observed ratio of the signals of two alleles, Aand B, is two to one, there are two possibilities. The first possibilityis that cancer cells have LOH with deletion of allele B in a sample with50% contamination with normal cells. The second possibility is thatthere is no LOH but allele A is duplicated in a sample with nocontamination with normal cells. The process begins at box 1500, wherethe following data are collected by the computing system; (1)sample-specific normalized signal intensities for both alleles of eachlocus and (2) assay-specific (specific for different SNP arrays and forsequence based approach) set of parameters defined based on analysis oflarge number of samples with known ASCN profiles. As described herein,any appropriate assay such as a SNP array-based assay orsequencing-based assay can be used to assess loci along a chromosome forhomozygosity or heterozygosity. In some cases, a system including asignal detector and a computer can be used to collect data (e.g.,fluorescent signals or sequencing results) regarding the homozygous orheterozygous nature of the plurality of loci (e.g., sample-specificnormalized signal intensities for both alleles of each locus). At box1510, allele specific copy numbers (ASCN) are reconstructed at eachlocus (e.g., each SNP). ASCNs are the numbers of copies of both paternaland maternal alleles. At box 1530, a likelihood function is used todetermine whether a homozygous locus or region of homozygous loci is dueto LOH. This can be conceptually analogous to a previously describedalgorithm designed to reconstruct total copy number (rather than ASCN)at each locus (e.g., SNP). See International Application No.PCT/US2011/026098 to Abkevish et al. The likelihood function can bemaximized over ASCN of all loci, level of contamination with benigntissue, total copy number averaged over the whole genome, and samplespecific noise level. At box 1540, an LOH region is determined as astretch of SNPs with one of the ASCNs (paternal or maternal) being zero.

FIG. 3 shows an exemplary process by which a computing system candetermine the presence or absence of an LOH signature. The processbegins at box 300, where data regarding the homozygous or heterozygousnature of a plurality of loci along a chromosome is collected by thecomputing system. As described herein, any appropriate assay such as aSNP array-based assay or sequencing-based assay can be used to assessloci along a chromosome for homozygosity or heterozygosity. In somecases, a system including a signal detector and a computer can be usedto collect data (e.g., fluorescent signals or sequencing results)regarding the homozygous or heterozygous nature of the plurality ofloci. At box 310, data regarding the homozygous or heterozygous natureof a plurality of loci as well as the location or spatial relationshipof each locus is assessed by the computing system to determine thelength of any LOH regions present along a chromosome. At box 320, dataregarding the number of LOH regions detected and the length of eachdetected LOH region is assessed by the computing system to determine thenumber of LOH regions that have a length (a) greater than or equal to apreset number of Mb (e.g., 15 Mb) and (b) less than the entire length ofthe chromosome containing that LOH region. At box 330, the computingsystem formats an output providing an indication of the presence orabsence of an LOH signature. Once formatted, the computing system canpresent the output to a user (e.g., a laboratory technician, clinician,or medical professional). As described herein, the presence or absenceof an LOH signature can be used to provide an indication about apatient's likely HDR status, an indication about the likely presence orabsence of genetic mutations in genes of the HDR pathway, and/or anindication about possible cancer treatment regimens.

FIG. 4 is a diagram of an example of a computer device 1400 and a mobilecomputer device 1450, which may be used with the techniques describedherein. Computing device 1400 is intended to represent various forms ofdigital computers, such as laptops, desktops, workstations, personaldigital assistants, servers, blade servers, mainframes, and otherappropriate computers. Computing device 1450 is intended to representvarious forms of mobile devices, such as personal digital assistants,cellular telephones, smart phones, and other similar computing devices.The components shown here, their connections and relationships, andtheir functions, are meant to be exemplary only, and are not meant tolimit implementations of the inventions described and/or claimed in thisdocument.

Computing device 1400 includes a processor 1402, memory 1404, a storagedevice 1406, a high-speed interface 1408 connecting to memory 1404 andhigh-speed expansion ports 1410, and a low speed interface 1415connecting to low speed bus 1414 and storage device 1406. Each of thecomponents 1402, 1404, 1406, 1408, 1410, and 1415, are interconnectedusing various busses, and may be mounted on a common motherboard or inother manners as appropriate. The processor 1402 can processinstructions for execution within the computing device 1400, includinginstructions stored in the memory 1404 or on the storage device 1406 todisplay graphical information for a GUI on an external input/outputdevice, such as display 1416 coupled to high speed interface 1408. Inother implementations, multiple processors and/or multiple buses may beused, as appropriate, along with multiple memories and types of memory.Also, multiple computing devices 1400 may be connected, with each deviceproviding portions of the necessary operations (e.g., as a server bank,a group of blade servers, or a multi-processor system).

The memory 1404 stores information within the computing device 1400. Inone implementation, the memory 1404 is a volatile memory unit or units.In another implementation, the memory 1404 is a non-volatile memory unitor units. The memory 1404 may also be another form of computer-readablemedium, such as a magnetic or optical disk.

The storage device 1406 is capable of providing mass storage for thecomputing device 1400. In one implementation, the storage device 1406may be or contain a computer-readable medium, such as a floppy diskdevice, a hard disk device, an optical disk device, or a tape device, aflash memory or other similar solid state memory device, or an array ofdevices, including devices in a storage area network or otherconfigurations. A computer program product can be tangibly embodied inan information carrier. The computer program product may also containinstructions that, when executed, perform one or more methods, such asthose described herein. The information carrier is a computer- ormachine-readable medium, such as the memory 1404, the storage device1406, memory on processor 1402, or a propagated signal.

The high speed controller 1408 manages bandwidth-intensive operationsfor the computing device 1400, while the low speed controller 1415manages lower bandwidth-intensive operations. Such allocation offunctions is exemplary only. In one implementation, the high-speedcontroller 1408 is coupled to memory 1404, display 1416 (e.g., through agraphics processor or accelerator), and to high-speed expansion ports1410, which may accept various expansion cards (not shown). In theimplementation, low-speed controller 1415 is coupled to storage device1406 and low-speed expansion port 1414. The low-speed expansion port,which may include various communication ports (e.g., USB, Bluetooth,Ethernet, or wireless Ethernet) may be coupled to one or moreinput/output devices, such as a keyboard, a pointing device, a scanner,an optical reader, a fluorescent signal detector, or a networking devicesuch as a switch or router, e.g., through a network adapter.

The computing device 1400 may be implemented in a number of differentforms, as shown in the figure. For example, it may be implemented as astandard server 1420, or multiple times in a group of such servers. Itmay also be implemented as part of a rack server system 1424. Inaddition, it may be implemented in a personal computer such as a laptopcomputer 1422. Alternatively, components from computing device 1400 maybe combined with other components in a mobile device (not shown), suchas device 1450. Each of such devices may contain one or more ofcomputing device 1400, 1450, and an entire system may be made up ofmultiple computing devices 1400, 1450 communicating with each other.

Computing device 1450 includes a processor 1452, memory 1464, aninput/output device such as a display 1454, a communication interface1466, and a transceiver 1468, among other components (e.g., a scanner,an optical reader, a fluorescent signal detector). The device 1450 mayalso be provided with a storage device, such as a microdrive or otherdevice, to provide additional storage. Each of the components 1450,1452, 1464, 1454, 1466, and 1468, are interconnected using variousbuses, and several of the components may be mounted on a commonmotherboard or in other manners as appropriate.

The processor 1452 can execute instructions within the computing device1450, including instructions stored in the memory 1464. The processormay be implemented as a chipset of chips that include separate andmultiple analog and digital processors. The processor may provide, forexample, for coordination of the other components of the device 1450,such as control of user interfaces, applications run by device 1450, andwireless communication by device 1450.

Processor 1452 may communicate with a user through control interface1458 and display interface 1456 coupled to a display 1454. The display1454 may be, for example, a TFT LCD (Thin-Film-Transistor Liquid CrystalDisplay) or an OLED (Organic Light Emitting Diode) display, or otherappropriate display technology. The display interface 1456 may compriseappropriate circuitry for driving the display 1454 to present graphicaland other information to a user. The control interface 1458 may receivecommands from a user and convert them for submission to the processor1452. In addition, an external interface 1462 may be provide incommunication with processor 1452, so as to enable near areacommunication of device 1450 with other devices. External interface 1462may provide, for example, for wired communication in someimplementations, or for wireless communication in other implementations,and multiple interfaces may also be used.

The memory 1464 stores information within the computing device 1450. Thememory 1464 can be implemented as one or more of a computer-readablemedium or media, a volatile memory unit or units, or a non-volatilememory unit or units. Expansion memory 1474 may also be provided andconnected to device 1450 through expansion interface 1472, which mayinclude, for example, a SIMM (Single In Line Memory Module) cardinterface. Such expansion memory 1474 may provide extra storage spacefor device 1450, or may also store applications or other information fordevice 1450. For example, expansion memory 1474 may include instructionsto carry out or supplement the processes described herein, and mayinclude secure information also. Thus, for example, expansion memory1474 may be provide as a security module for device 1450, and may beprogrammed with instructions that permit secure use of device 1450. Inaddition, secure applications may be provided via the SIMM cards, alongwith additional information, such as placing identifying information onthe SIMM card in a non-hackable manner.

The memory may include, for example, flash memory and/or NVRAM memory,as discussed below. In one implementation, a computer program product istangibly embodied in an information carrier. The computer programproduct contains instructions that, when executed, perform one or moremethods, such as those described herein. The information carrier is acomputer- or machine-readable medium, such as the memory 1464, expansionmemory 1474, memory on processor 1452, or a propagated signal that maybe received, for example, over transceiver 1468 or external interface1462.

Device 1450 may communicate wirelessly through communication interface1466, which may include digital signal processing circuitry wherenecessary. Communication interface 1466 may provide for communicationsunder various modes or protocols, such as GSM voice calls, SMS, EMS, orMMS messaging, CDMA, TDMA, PDC, WCDMA, CDMA2000, or GPRS, among others.Such communication may occur, for example, through radio-frequencytransceiver 1468. In addition, short-range communication may occur, suchas using a Bluetooth, WiFi, or other such transceiver (not shown). Inaddition, GPS (Global Positioning System) receiver module 1470 mayprovide additional navigation- and location-related wireless data todevice 1450, which may be used as appropriate by applications running ondevice 1450.

Device 1450 may also communicate audibly using audio codec 1460, whichmay receive spoken information from a user and convert it to usabledigital information. Audio codec 1460 may likewise generate audiblesound for a user, such as through a speaker, e.g., in a handset ofdevice 1450. Such sound may include sound from voice telephone calls,may include recorded sound (e.g., voice messages, music files, etc.) andmay also include sound generated by applications operating on device1450.

The computing device 1450 may be implemented in a number of differentforms, as shown in the figure. For example, it may be implemented as acellular telephone 1480. It may also be implemented as part of asmartphone 1482, personal digital assistant, or other similar mobiledevice.

Various implementations of the systems and techniques described hereincan be realized in digital electronic circuitry, integrated circuitry,specially designed ASICs (application specific integrated circuits),computer hardware, firmware, software, and/or combinations thereof.These various implementations can include implementation in one or morecomputer programs that are executable and/or interpretable on aprogrammable system including at least one programmable processor, whichmay be special or general purpose, coupled to receive data andinstructions from, and to transmit data and instructions to, a storagesystem, at least one input device, and at least one output device.

These computer programs (also known as programs, software, softwareapplications or code) include machine instructions for a programmableprocessor, and can be implemented in a high-level procedural and/orobject-oriented programming language, and/or in assembly/machinelanguage. As used herein, the terms “machine-readable medium” and“computer-readable medium” refer to any computer program product,apparatus and/or device (e.g., magnetic discs, optical disks, memory,and Programmable Logic Devices (PLDs)) used to provide machineinstructions and/or data to a programmable processor, including amachine-readable medium that receives machine instructions as amachine-readable signal. The term “machine-readable signal” refers toany signal used to provide machine instructions and/or data to aprogrammable processor.

To provide for interaction with a user, the systems and techniquesdescribed herein can be implemented on a computer having a displaydevice (e.g., a CRT (cathode ray tube) or LCD (liquid crystal display)monitor) for displaying information to the user and a keyboard and apointing device (e.g., a mouse or a trackball) by which the user canprovide input to the computer. Other kinds of devices can be used toprovide for interaction with a user as well; for example, feedbackprovided to the user can be any form of sensory feedback (e.g., visualfeedback, auditory feedback, or tactile feedback); and input from theuser can be received in any form, including acoustic, speech, or tactileinput.

The systems and techniques described herein can be implemented in acomputing system that includes a back end component (e.g., as a dataserver), or that includes a middleware component (e.g., an applicationserver), or that includes a front end component (e.g., a client computerhaving a graphical user interface or a Web browser through which a usercan interact with an implementation of the systems and techniquesdescribed herein), or any combination of such back end, middleware, orfront end components. The components of the system can be interconnectedby any form or medium of digital data communication (e.g., acommunication network). Examples of communication networks include alocal area network (“LAN”), a wide area network (“WAN”), and theInternet.

The computing system can include clients and servers. A client andserver are generally remote from each other and typically interactthrough a communication network. The relationship of client and serverarises by virtue of computer programs running on the respectivecomputers and having a client-server relationship to each other.

In some cases, a computing system provided herein can be configured toinclude one or more sample analyzers. A sample analyzer can beconfigured to produce a plurality of signals about genomic DNA of atleast one pair of human chromosomes of a cancer cell. For example, asample analyzer can produce signals that are capable of beinginterpreted in a manner that identifies the homozygous or heterozygousnature of loci along a chromosome. In some cases, a sample analyzer canbe configured to carry out one or more steps of a SNP array-based assayor sequencing-based assay and can be configured to produce and/orcapture signals from such assays. In some cases, a computing systemprovided herein can be configured to include a computing device. In suchcases, the computing device can be configured to receive signals from asample analyzer. The computing device can include computer-executableinstructions or a computer program (e.g., software) containingcomputer-executable instructions for carrying out one or more of themethods or steps described herein. In some cases, suchcomputer-executable instructions can instruct a computing device toanalyze signals from a sample analyzer, from another computing device,from a SNP array-based assay, or from a sequencing-based assay. Theanalysis of such signals can be carried out to determine genotypes,homozygosity at certain loci, regions of homozygosity, the number of LOHregions, to determine the size of LOH regions, to determine the numberof LOH regions having a particular size or range of sizes, to determinewhether or not a sample is positive for an LOH signature, to determinethe number of Indicator LOH Regions in at least one pair of humanchromosomes, to determine a likelihood of a deficiency in BRCA1 and/orBRCA2 genes, to determine a likelihood of a deficiency in HDR, todetermine a likelihood that a cancer patient will respond to aparticular cancer treatment regimen (e.g., a regimen that includes a DNAdamaging agent, an anthracycline, a topoisomerase I inhibitor,radiation, a PARP inhibitor, or a combination thereof), or to determinea combination of these items.

In some cases, a computing system provided herein can includecomputer-executable instructions or a computer program (e.g., software)containing computer-executable instructions for formatting an outputproviding an indication about the number of LOH regions, the size of LOHregions, the number of LOH regions having a particular size or range ofsizes, whether or not a sample is positive for an LOH signature, thenumber of Indicator LOH Regions in at least one pair of humanchromosomes, a likelihood of a deficiency in BRCA1 and/or BRCA2 genes, alikelihood of a deficiency in HDR, a likelihood that a cancer patientwill respond to a particular cancer treatment regimen (e.g., a regimenthat includes a DNA damaging agent, an anthracycline, a topoisomerase Iinhibitor, radiation, a PARP inhibitor, or a combination thereof), or acombination of these items. In some cases, a computing system providedherein can include computer-executable instructions or a computerprogram (e.g., software) containing computer-executable instructions fordetermining a desired cancer treatment regimen for a particular patientbased at least in part on the presence or absence of an LOH signature oron the number of Indicator LOH Regions.

In some cases, a computing system provided herein can include apre-processing device configured to process a sample (e.g., cancercells) such that a SNP array-based assay or sequencing-based assay canbe performed. Examples of pre-processing devices include, withoutlimitation, devices configured to enrich cell populations for cancercells as opposed to non-cancer cells, devices configured to lyse cellsand/or extract genomic nucleic acid, and devices configured to enrich asample for particular genomic DNA fragments.

This document also provides kits for assessing samples (e.g., cancercells) as described herein. For example, this document provides kits forassessing cancer cells for the presence of an LOH signature or todetermine the number of Indicator LOH Regions in at least one pair ofhuman chromosomes. A kit provided herein can include either SNP probes(e.g., an array of SNP probes for carrying out a SNP array-based assaydescribed herein) or primers (e.g., primers designed for sequencing SNPregions via a sequencing-based assay) in combination with a computerprogram product containing computer-executable instructions for carryingout one or more of the methods or steps described herein (e.g.,computer-executable instructions for determining the number of LOHregions having a particular size or range of sizes). In some cases, akit provided herein can include at least 500, 1000, 10,000, 25,000, or50,000 SNP probes capable of hybridizing to polymorphic regions of humangenomic DNA. In some cases, a kit provided herein can include at least500, 1000, 10,000, 25,000, or 50,000 primers capable of sequencingpolymorphic regions of human genomic DNA. In some cases, a kit providedherein can include one or more other ingredients for performing a SNParray-based assay or a sequencing-based assay. Examples of such otheringredients include, without limitation, buffers, sequencingnucleotides, enzymes (e.g., polymerases), etc. This document alsoprovides the use of any appropriate number of the materials providedherein in the manufacture of a kit for carrying out one or more of themethods or steps described herein. For example, this document providesthe use of a collection of SNP probes (e.g., a collection of 10,000 to100,000 SNP probes) and a computer program product provided herein inthe manufacture of a kit for assessing cancer cells for the presence ofan LOH signature. As another example, this document provides the use ofa collection of primers (e.g., a collection of 10,000 to 100,000 primersfor sequencing SNP regions) and a computer program product providedherein in the manufacture of a kit for assessing cancer cells for thepresence of an LOH signature.

The invention will be further described in the following examples, whichdo not limit the scope of the invention described in the claims.

EXAMPLES Example 1—Assessing LOH Regions and HDR

Two sets of tumors were used from advanced ovarian cancer patients. Thefirst set of 94 tumors (training set) was used to derive a candidatesignature, and the second set of 40 tumors (validation set) was used tovalidate the signature. All coding regions of BRCA1 and BRCA2 genes weresequenced to detect germ line and somatic mutations. Levels of BRCA1 andBRCA2 mRNA expression were measured, and Affymetrix SNP microarrays wereperformed.

A computer program was used to reconstruct LOH signature status based onallele intensities derived from the microarray data. An algorithm wasdeveloped and implemented as a computer program to reconstruct LOHregions based on genotype (e.g., SNP genotype) data.

One point of the algorithm was to first reconstruct allele specific copynumbers (ASCN) at each locus (e.g., SNP). ASCNs are the numbers ofcopies of both paternal and maternal alleles. An LOH region was thendetermined as a stretch of SNPs with one of the ASCNs (paternal ormaternal) being zero. The algorithm was based on maximizing a likelihoodfunction and was conceptually analogous to a previously describedalgorithm designed to reconstruct total copy number (rather than ASCN)at each locus (e.g., SNP). See International Application No.PCT/US2011/026098 to Abkevish et al. The likelihood function wasmaximized over ASCN of all loci, level of contamination with benigntissue, total copy number averaged over the whole genome, and samplespecific noise level. The input data for the algorithm included (1)sample-specific normalized signal intensities for both allele of eachlocus and (2) assay-specific (specific for different SNP arrays and forsequence based approach) set of parameters defined based on analysis oflarge number of samples with known ASCN profiles.

Tumors were defined as being HDR deficient for the purpose of thisanalysis if they either had one or more deleterious mutations in BRCA1and/or BRCA2 genes or if they had low expression of BRCA1 mRNA. The restof the tumors were defined as likely HDR non-deficient for the purposeof this analysis.

The distribution of the lengths of LOH regions was investigated (FIG.5). Three categories of LOH regions were used: (1) LOH affecting a wholechromosome; (2) large LOH regions (greater than about 15 Mb), whichtypically affect a part of a chromosomal arm or the whole chromosomalarm; and (3) multiple short LOH regions (less than about 15 Mb). Second,using the training set only, the number of LOH regions of one of thesethree categories was assessed for possible correlations with HDRdeficiency. It was discovered that (1) the number of short LOH regionsdid not significantly correlate with HDR deficiency (p>0.05); (2) LOHcovering an entire chromosome correlated weakly with HDR deficiency(p=0.0011); and (3) the number of large LOH regions correlatedsignificantly with HDR deficiency (p=1.9e-8). More specifically, it wasdiscovered that all HDR deficient tumors had a high number of large LOHregions (e.g., nine or more), while the majority of tumors likely to beHDR non-deficient had a small number of large LOH regions (FIGS. 6-8).It was probable that tumors likely to be HDR non-deficient were in factHDR deficient due to other genetic alterations, excluding BRCA1 andBRCA2 mutations and low mRNA expression. In addition to the number oflarge LOH regions, the total length of these regions also correlatedsignificantly with HDR deficiency.

These results were confirmed with the validation set: (1) the number ofshort LOH regions did not significantly correlate with HDR deficiency(p>0.05); (2) LOH covering an entire chromosome correlated weakly withHDR deficiency (p=0.05); and (3) the number of large LOH regionscorrelated significantly with HDR deficiency (p=3.9e-6).

The 134 tumors were divided from combined training and validation datasets into three groups: (1) BRCA deficient if they either had one ormore deleterious mutations in BRCA1 and/or BRCA2 genes or if they hadlow expression of BRCA1 mRNA; (2) HDR deficient/BRCA intact if they have9 or more large LOH regions (greater than 15 Mb but less than the lengthof the entire chromosome); (3) HDR intact if they have less than 9 largeLOH regions (greater than 15 Mb but less than the length of the entirechromosome). Results of this analysis are presented in FIG. 9. It showsa high frequency of BRCA deficiency as well as HDR deficiency that isnot due to BRCA deficiency among ovarian tumors.

FIG. 10 shows the distribution of large LOH regions (greater than 15 Mbbut less than the length of the entire chromosome) for different typesof cancer cell lines. The size of the circles is proportional to thenumber of samples with such number of large LOH regions. Frequency ofHDR deficiency (cell lines with at least 9 of such large LOH regions) isthe highest among breast and esophagus cancer cell lines. No HDRdeficiency was observed among colon cancer cell lines. Validating theprevious findings for ovarian tumors, all BRCA deficient cell lines werefound to be HDR deficient as well.

FIG. 11 shows the distribution of large LOH regions (greater than 15 Mbbut less than the length of the entire chromosome) for publiclyavailable lung tumor data set (GSE19399 from Gene Expression Omnibus).It was observed that frequency of HDR deficiency (defined as having atleast 9 large LOH regions) is quite large among lung tumors (39%).

In FIG. 12 the results of analysis of different tumors and cell linesare summarized. Frequency of HDR deficiency defined as fraction ofsamples with at least 9 large LOH regions (greater than 15 Mb but lessthan the length of the entire chromosome) is presented for severaltumors and cell lines. This frequency is as high as 50% among ovariantumors and was not observed at all among brain and colon cell lines.Thus it appears that HDR deficiency plays an important role for themajority of cancers.

Example 2—Chemo Toxicity Responses

In preparation of chemo toxicity response experiments, all cell lineswere grown at 37° C. plus 5% CO₂ in 75 cm² tissue culture flasks (VWRInternational, Inc. Cat #353136) and the recommended growth medium.Before performing each experiment, each cell line was trypsinized(Invitrogen Corporation Cat #25200-056), counted, and seeded in AdvancedRPMI 1640 (Invitrogen Corporation Cat #12633-020), 3% FBS, 1%penicillin/streptomycin (Invitrogen Corporation Cat #15140-122) at 2500cells or 5000 cells in 100 μL media per well from columns 2-12 of96-well polystyrene microplates with clear bottom (Perkin Elmer Cat#6005181), leaving column 1 with 100 μL per well of media only. Thecell-seeded plates were then incubated at 37° C. plus 5% CO₂ overnight.

Two different final drug concentration working stocks were prepared. Incases where 100% DMSO was required for drug solubility, Advanced RPMI1640 was used as the diluent for the highest concentration. AdvancedRPMI 1640 plus a predetermined amount of DMSO equal to the total DMSO inthe high concentration working stock was used for the low concentration,with a maximum of 60% DMSO used for the lowest concentration. This wasdone to keep the DMSO concentrations equal in every well and preventnon-specific cell death as a result of DMSO. The lower of the two drugconcentrations was placed in a 96-well, thin-wall PCR cycle plate(Robbins Scientific Cat #1055-00-0) in rows A-D, column 12, while thehigher concentration was placed in rows E-H, column 12, of the sameplate. Serial dilutions of 1:2 or 1:3 were performed in a descendingmanner from column 12 to 3, leaving columns 1 and 2 to be used for nocell/no drug and no drug controls. This allowed for quadruplet datapoints for each drug concentration. Once dilutions were complete, 5 μLwas transferred from the dilution plate to the corresponding well of theseeded cell plate. Plates receiving drugs were then incubated at 37° C.plus 5% CO₂ for either 3 days or 6 days.

Following a 3-day or 6-day dose regimen, ATPlite assays (Perkin Elmercat #6016941) were run on each well of each plate according to theATPLite Assay protocol. The luminescence was then read on a FUSIONmachine and saved as a .CSV file. For each cell-line and drugcombination, the four replicates of the no-drug control were averagedand divided by 100 to create a “normalization factor” used to calculatea normalized percent survival. The normalized percent survival for theno-drug controls was 100%. The four replicates of the cell-plus-drugwells were averaged and divided by the normalization factor for eachdrug concentration. The percent survival for each drug concentration,starting with a concentration equal to 0, was used to calculate an IC₅₀using proprietary software.

FIG. 13 shows response to chemotherapy for breast and ovarian cancercell lines. On y-axis are indicated values of Log₁₀(IC₅₀) for differentchemotherapy drugs (camptothecin, as well as averaged results forplatinum compounds (oxaliplatin, cisplatin, and carboplatin) oranthracyclines (doxorubicin and epirubicin)) when exposed to 29 breastcancer cell lines as well as Log₁₀(IC₅₀) of paclitaxel when exposed to27 ovarian cancer cell lines. On the x-axis the number of large LOHregions longer than 15 Mb and shorter than the entire chromosome areindicated for these cell lines. The dashed lines place a thresholdnumber at nine.

FIG. 14 is a version of a graph from FIG. 13 that indicates specificityand sensitivity among responders and non-responders to treatment withplatinum compounds (oxaliplatin, cisplatin, and carboplatin) whenexposed to 29 breast cancer cell lines. The dashed lines place athreshold number of large LOH regions longer than 15 Mb and shorter thanthe entire chromosome at nine. The solid line divides cell lines intoresponders and non-responders.

OTHER EMBODIMENTS

It is to be understood that while the invention has been described inconjunction with the detailed description thereof, the foregoingdescription is intended to illustrate and not limit the scope of theinvention, which is defined by the scope of the appended claims. Otheraspects, advantages, and modifications are within the scope of thefollowing claims.

What is claimed is:
 1. A method of treating cancer, comprising:predicting a cancer patient's response to a cancer treatment regimencomprising a DNA damaging agent, an anthracycline, a topoisomerase Iinhibitor, radiation, and/or a PARP inhibitor, wherein predicting thecancer patient's response to the cancer treatment regimen comprises:determining, in genomic DNA derived from a cancer cell obtained from thepatient, the total number of LOH regions in at least one pair of humanchromosomes of said DNA that are longer than a first length but shorterthan the length of the whole chromosome containing the LOH region,wherein said at least one pair of human chromosomes is not a human X/Ysex chromosome pair, wherein said first length is about 1.5 or moremegabases and wherein the cancer cell is selected from the groupconsisting of breast cancer cells, ovarian cancer cells, leukemia cancercells, esophageal cancer cells, lung cancer cells, and prostate cancercells; correlating said total number of LOH regions that is greater thana reference number that is at least 6 with an increased likelihood thatsaid cancer patient will respond to said cancer treatment regimen; andbased on the correlating of said total number of LOH regions with anincreased likelihood that said cancer patient will respond to saidcancer treatment regimen, administering to the cancer patient atreatment regimen comprising a DNA damaging agent, an anthracycline, atopoisomerase I inhibitor, radiation, and/or a PARP inhibitor.
 2. Themethod of claim 1, wherein said LOH regions are determined in at leastten pairs of human chromosomes.
 3. The method of claim 1, wherein saidtotal number of LOH regions.
 4. The method of claim 1, wherein saidfirst length is about 6 or more megabases.
 5. The method of claim 1,wherein said reference number is at least
 8. 6. The method of claim 1,wherein said at least one pair of human chromosomes is not humanchromosome
 17. 7. The method of claim 1, wherein said DNA damaging agentis cisplatin, carboplatin, oxalaplatin, or picoplatin, saidanthracycline is epirubicin or doxorubicin, said topoisomerase Iinhibitor is campothecin, topotecan, or irinotecan, or said PARPinhibitor is iniparib, olaparib or veliparib.
 8. A method of treatingcancer, comprising: predicting a cancer patient's response to atreatment regimen including paclitaxel or docetaxel, wherein predictingthe cancer patient's response to a treatment regimen comprises:determining, in genomic DNA derived from a cancer cell obtained from thepatient, the total number of LOH regions in at least one pair of humanchromosomes of said DNA that are longer than a first length but shorterthan the length of the whole chromosome containing the LOH region,wherein said at least one pair of human chromosomes is not a human X/Ysex chromosome pair, wherein said first length is about 1.5 or moremegabases, wherein the cancer cell is selected from the group consistingof breast cancer cells, ovarian cancer cells, leukemia cancer cells,esophageal cancer cells, lung cancer cells, and prostate cancer cells;correlating said total number of LOH regions that is greater than areference number that is at least 6 with an increased likelihood thatsaid cancer patient will not respond to a treatment regimen includingpaclitaxel or docetaxel; and based on the correlating of said totalnumber of LOH regions with an increased likelihood that said cancerpatient will respond to said cancer treatment regimen, administering tothe patient a treatment regimen including a DNA damaging agent, ananthracycline, a topoisomerase I inhibitor, radiation, and/or a PARPinhibitor.
 9. The method of claim 8, wherein said LOH regions aredetermined in at least ten pairs of human chromosomes.
 10. The method ofclaim 8, wherein said total number of LOH regions is 9 or more.
 11. Themethod of claim 8, wherein said first length is 6 or more megabases. 12.The method of claim 8, wherein said reference number is at least
 8. 13.The method of claim 8, wherein said at least one pair of humanchromosomes is not human chromosome 17.